I have a 2009 model Honda unicorn motorcycle. It's very difficult to ride during rain or cold weather, because of missing. I asked service center but they did not do anything. I have changed the CDI, ignition coil and air filter but the problem persists.

To diagnose cracked wires, its best to check it late at night when you can see the tiny sparks earthing against the engine case/frame. If the engine is dry use a small spray gun to lightly mist the wires, you should see faint arcs of electricity as they earth to the case/frame instead of arcing in the spark plug
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MauroJun 10 '13 at 19:41

Sounds like you're on the right track. Water/cold missing issues are usually ignition related. I've been down this road a number of times myself. It can be quite hard to pinpoint. Look for cracked ignition components that might be letting water in/support condensation.

Another (but somewhat remote possibility) is water in the fuel. Bad seal on the gas tank?